GROMACS version: 2019
GROMACS modification: No
Dear all,
I am going to due some simulations for protein in different organic solvents. I follow the procedure in this link, but when I checked the obtained .gro file in VMD, it seems that the solvent are located in the edge of the box is broken. Do you have any idea? (I mean the dot particles around the box of the following image)
What you are seeing is the normal consequence of periodic boundary conditions. Make molecules whole with trjconv.
Dear Jalemkul,
Thank you very much for your response.
Dear Sir,
As a newcomer to GROMACS, I’ve been attempting to create a solvent box following a tutorial(you give in your previous message), but I’ve encountered some difficulties in achieving the desired result specifically for acetone. I understand that you have successfully created solvent boxes in the past and I would greatly appreciate your assistance in understanding the steps involved in generating an acetone solvent box.
Could you kindly provide a detailed explanation of the procedure you used to create the acetone solvent box? Any insights or tips you can offer would be immensely helpful for me to progress with my simulations effectively.
I look forward to your response.
Best regards,
Lukhmanul hakeem k
Dear Lukhmanul,
If you have the structure and the topology of your molecules, you can use gmx insert-molecules to fill the box with the solvent of interest. You can have more information on gmx insert-molecules by looking at the GROMACS manual here and by reading the tool’s help with gmx insert-molecules --h. As a guide, you can follow this very good tutorial about building a biphasic system and plug in it a small protein. In your case you may just want to just plug in your solute of interest and keep the box monophasic.